Search on enable-mpi? I saw one possibly useful 2017 response/suggestion from dac on this.
<div>-------- Original message --------</div><div>From: Sundar <jubilantsundar.gmail.com> </div><div>Date:12/23/2018 10:40 AM (GMT-08:00) </div><div>To: David Case <david.case.rutgers.edu>, AMBER Mailing List <amber.ambermd.org> </div><div>Subject: Re: [AMBER] Amber18 compilation error on a Linux CPU cluster </div><div>
</div>I rerun everything from the tar files.
Serial installation was successful but mpi compilation fails with following
errors
sundar.name:~/tools/amber18/amber18> ./configure -mpi gnu
Checking for updates...
Checking for available patches online. This may take a few seconds...
Available AmberTools 18 patches:
No patches available
Available Amber 18 patches:
No patches available
AMBER_PREFIX=/u/sundar/tools/amber18/amber18
AMBER_SOURCE=/u/sundar/tools/amber18/amber18
Using the AmberTools miniconda installation in
/u/sundar/tools/amber18/amber18/miniconda
version 2.7.13
Obtaining the gnu compiler suite versions, e.g.:
gcc -v
The C version is 4.9.2
The Fortran version is 4.9.2
Testing the gcc compiler:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp testp.c
OK
Testing the g++ compiler:
g++ -fPIC -o testp testp.cpp
OK
Testing the gfortran compiler:
gfortran -fPIC -O0 -o testp testp.f
OK
Testing mixed C/Fortran compilation:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -c -o testp.c.o
testp.c
gfortran -fPIC -O0 -c -o testp.f.o testp.f
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o testp
testp.c.o testp.f.o -lgfortran -w
OK
Testing pointer size:
gcc -fPIC -D_FILE_OFFSET_BITS=64 -D_LARGEFILE_SOURCE -o
test_pointer_size test_pointer_size.c
Detected 64 bit operating system.
Testing flex: OK
Checking NetCDF...
Using bundled NetCDF library.
Using existing NetCDF in '/u/sundar/tools/amber18/amber18'
Checking for zlib: OK
Checking for libbz2: OK
Testing the g++ compiler with boost:
g++ -fPIC testp.cpp -lboost_thread -lboost_system -o testp
Warning: Could not link to boost. Ensure boost-thread, boost-system and
boost headers are installed.
Warning: Failed command:
g++ -fPIC -lboost_thread -lboost_system -o testp testp.cpp
Warning: Check boost.compile.err for error details.
Warning: Memembed functionality in packmol_memgen not available.
Configuring fftw-3.3 (may be time-consuming)...
Error: FFTW configure returned 1
FFTW configure failed! Check the fftw3_config.log file
in the /u/sundar/tools/amber18/amber18/AmberTools/src directory.
Configure failed due to the errors above!
$ tail $AMBERHOME/AmberTools/src/fftw3_config.log
checking for mpicc... no
checking for hcc... no
checking for mpcc... no
checking for mpcc_r... no
checking for mpxlc... no
checking for cmpicc... no
checking for MPI_Init... no
checking for MPI_Init in -lmpi... no
checking for MPI_Init in -lmpich... no
configure: error: could not find mpi library for --enable-mpi
Thanks,
J
On Sun, Dec 23, 2018 at 7:37 AM David Case <david.case.rutgers.edu> wrote:
> On Sat, Dec 22, 2018, Sundar wrote:
>
> >I did the serial installation first and then did "./configure -mpi gnu".
> >That's when I got this error message.
>
> What I don't understand is why you were not prompted to apply the
> updates when you did the original serial installation.
>
> >
> >Would you recommend a fresh serial installation from the tar files and try
> >the parallel version?
>
> Yes....good luck....dac
>
>
--
Thanks,
Sundar Thangapandian
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Received on Sun Dec 23 2018 - 11:30:02 PST
